Link to this post | posted 15 Feb, 2022 16:28

pia1@pitt.edu

Hi Chris, Thanks so much for the in-depth discussion/explanation and advice! I really appreciate it! I wouldn't claim to have extensive experience with bioinformatics tools, but I am fully aware that no computational tool is 100% perfect. And chances are there are minor issues that are not necessarily worth fixing. In this case, I do NOT think the program "failed" at all. I'm just glad that I got clarifications from experts like you and thank you for putting this great tool to work in the first place!

Link to this post | posted 11 Feb, 2022 18:55
pia1@pitt.edu	Thank you both for replying! I agree with you, Debbie. Starterator by itself does not have all the answers. In this case, one of the two starts with the same number of MAs is actually not present in this gene. It really does not affect our analysis but I think we're just being extra nuanced. I'll email you to set up a time to chat.

Link to this post | posted 10 Feb, 2022 18:20
pia1@pitt.edu	Hi, This is regarding Pytheas gene 29 in the current version of Starterator report as of 02/10/22. My student caught the following and asked why start 44 is not the most annotated start since it has the same number of manual annotation as start 39. Please see attached slide for details. I don’t have the answer and would appreciate your input. Thank you! Ping An from University of Pittsburgh 349Kb

Link to this post | posted 18 Dec, 2021 14:48
pia1@pitt.edu	Thank you! Debbie. That is very helpful.

Link to this post | posted 17 Dec, 2021 14:19

pia1@pitt.edu

This is Ping An at University of Pittsburgh. I'm considering the function calls for genes 2, 3 and 4 of Meyran as terminase, 1 small subunit (gene 2) and 2 large subunits for ATPase domain (gene 3) and nuclease domain (gene 4), respectively. These tentative function calls are consistent with the current consensus for cluster DT phages. But I have some doubts, which seem to echo the two posts above. For gene 2, the best HHpred hit supporting terminase small subunit has a coverage of 45%. For gene 3, the top 5 strongest HHpred hits (probability over 90% and coverage at least 70%) are ATPase. Among these 5, 3 are also nuclease. For gene 4, top 10 strongest HHpred hits (probability over 90% and coverage at least 70%) are nuclease. Among these 10, 3 are also ATPase. Based on the above HHpred analysis, 1. Should gene 2 be assigned the function as “terminase small subunit”? 2. Should gene 3 and 4 be assigned specifically as terminase large subunit (ATPase) and (nuclease), respectively? I hope someone may provide some insights on the issue.

Link to this post | posted 30 Sep, 2021 21:26

pia1@pitt.edu

Hi, This is Ping An at University of Pittsburgh. I need some help understanding the minor tail protein gene called in the left arm of CS3 phages. The phamerator image in the attached slide should help to clarify which minor tail protein genes (highlighted in red ovals) are being discussed below. I've noticed that a minor tail protein was called immediately downstream of the portal protein in the left arm in several CS3 phages including Guillaume, Newt and Lucker. This seems puzzling to me since they are not cluster A phages in which you may expect minor tail proteins in the left arm. It turns out that the minor tail protein genes in the above 3 phages have high nucleotide similarity to gene 34 (with the minor tail protein function assignment) in phage Asapag of cluster DN1. My questions are, first, should gene 34 in Asapag be assigned the function as minor tail protein? second, if Asapag gene 34 indeed should be called a minor tail protein, then can we assign the same to the similar genes in the left arm of CS3 phages? Thank you in advance for your help and insights! I look forward to your response! 140Kb